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xie186 / ViewBS

ViewBS - a powerful toolkit for visualization of high-throughput bisulfite sequencing data
GNU General Public License v3.0
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methcoverage only shows one dot #60

Closed RRebo closed 2 years ago

RRebo commented 3 years ago

Hi, I have used methcoverage before, and it did work well. Now, with a new set of data, while all the other commands are working, I get a one dot graph for each of my samples on the methcoverage graph. I added the metcoverage folder created during the run and here is one of my CG_report files: https://drive.google.com/file/d/1BumWLr8brd4sPSx6OVRk37tfuAlAnacK/view?usp=sharing

~/ViewBS-0.1.9/ViewBS MethCoverage --reference Hd_genome_1.0.fasta --sample St-1-calyx-60-d_S4_R1_001_val_1_bismark_bt2_pe.sorted.deduplicated.CpG_report.txt.gz,St1calyx60d --sample St-1-calyx-57-e_R1_001_val_1_bismark_bt2_pe.sorted.deduplicated.CpG_report.txt.gz,St1Calyx57e --sample St-1-calyx-63-f_R1_001_val_1_bismark_bt2_pe.sorted.deduplicated.CpG_report.txt.gz,St1Calyx63f --sample St-1-thorax-5-j_R1_001_val_1_bismark_bt2_pe.sorted.deduplicated.CpG_report.txt.gz,St1Thorax5j --sample St-3-calyx-37-b_R1_001_val_1_bismark_bt2_pe.sorted.deduplicated.CpG_report.txt.gz,St3Calyx37b --sample St-3-calyx-58-a_R1_001_val_1_bismark_bt2_pe.sorted.deduplicated.CpG_report.txt.gz,St3Calyx58a --sample St-3-calyx-60-c_R1_001_val_1_bismark_bt2_pe.sorted.deduplicated.CpG_report.txt.gz,St3Calyx60c --sample St-3-thorax-5-g_R1_001_val_1_bismark_bt2_pe.sorted.deduplicated.CpG_report.txt.gz,St3Thorax5g --sample St-3-thorax-5-h_R1_001_val_1_bismark_bt2_pe.sorted.deduplicated.CpG_report.txt.gz,St3Thorax5h --sample St-3-thorax-5-i_R2_val_1_bismark_bt2_pe.sorted.deduplicated.CpG_report.txt.gz,St3Thorax5i --outdir metCoverage --prefix EpiHypo

ViewBS.zip

Thank you Rita

Kennyluo4 commented 3 years ago

I have similar issue. Seems it adds up the CG sites from all samples as the denominator. I got over 70% sites with at least 1 coverage when plotting just 1 sample. It dropped to less than 30% when I submitted 3 samples. And I got just 1 dot for each sample when using 9 samples.
MethCoverage plot is very confusing, the histogram output from Methylkit is more straightforward.

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xie186 commented 2 years ago

Thanks for using ViewBS. I'll add warnings when ViewBS encounters similar patterns.